fix(hooks): auto-stage .gemini, .claude, .codex directories on commit

- Remove .claude from .gitignore so it can be tracked alongside .gemini and .codex
- Add auto-staging logic to pre-commit hook for AI agent config directories
- Update setup-pre-commit-hook.js to include AI dir staging in generated hook
- Auto-configure core.hooksPath in setup script instead of requiring manual step

Previously the pre-commit hook only staged .knowledge directories. The .claude
directory was also listed in .gitignore, making it impossible to track. The setup
script required a manual `git config core.hooksPath .githooks` step that was
easy to forget, causing all hooks (including pre-push session backup) to never
activate.

Fixes #170

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

Author: konard

.githooks/pre-commit

@@ -15,6 +15,15 @@ done < <(
     -print0
 )
 
+# CHANGE: auto-stage AI agent config directories (.gemini, .claude, .codex)
+# WHY: ensures AI session context is always included in commits without manual git add
+# REF: issue-170
+for ai_dir in .gemini .claude .codex; do
+  if [ -d "$ai_dir" ]; then
+    git add -A -- "$ai_dir"
+  fi
+done
+
 MAX_BYTES=$((99 * 1000 * 1000))
 too_large=()
 

.gitignore

@@ -23,4 +23,3 @@ yarn-error.log*
 pnpm-debug.log*
 reports/
 .idea
-.claude

experiments/test-pre-commit-ai-dirs.sh

@@ -0,0 +1,49 @@
+#!/usr/bin/env bash
+set -euo pipefail
+
+# Test that the pre-commit hook logic correctly stages AI config directories
+echo "=== Testing AI directory auto-staging logic ==="
+
+REPO_ROOT="$(git rev-parse --show-toplevel)"
+cd "$REPO_ROOT"
+
+# Create test AI directories with test files
+for ai_dir in .gemini .claude .codex; do
+  mkdir -p "$ai_dir"
+  echo "test-content-$(date +%s)" > "$ai_dir/test-file.txt"
+done
+
+echo "Created test files:"
+ls -la .gemini/test-file.txt .claude/test-file.txt .codex/test-file.txt
+
+# Check gitignore status
+echo ""
+echo "=== Checking gitignore status ==="
+for ai_dir in .gemini .claude .codex; do
+  if git check-ignore -q "$ai_dir/test-file.txt" 2>/dev/null; then
+    echo "IGNORED: $ai_dir (this is a problem!)"
+  else
+    echo "NOT IGNORED: $ai_dir (good - can be tracked)"
+  fi
+done
+
+# Simulate the auto-staging logic from the pre-commit hook
+echo ""
+echo "=== Simulating auto-staging ==="
+for ai_dir in .gemini .claude .codex; do
+  if [ -d "$ai_dir" ]; then
+    git add -A -- "$ai_dir"
+    echo "Staged: $ai_dir"
+  fi
+done
+
+echo ""
+echo "=== Staged files ==="
+git diff --cached --name-only | grep -E "^\.(gemini|claude|codex)/" || echo "(none found)"
+
+# Clean up - unstage the test files
+git reset HEAD -- .gemini .claude .codex 2>/dev/null || true
+rm -rf .gemini/test-file.txt .claude/test-file.txt .codex/test-file.txt
+
+echo ""
+echo "=== Test complete ==="

scripts/setup-pre-commit-hook.js

@@ -1,7 +1,9 @@
 #!/usr/bin/env node
 
-// CHANGE: Add repeatable pre-commit hook setup for secret auto-redaction
-// WHY: Keep secret scanning on every commit without one-time manual hook wiring.
+// CHANGE: Add repeatable pre-commit hook setup for secret auto-redaction and AI session directory staging
+// WHY: Keep secret scanning on every commit without one-time manual hook wiring,
+//      and automatically include .gemini, .claude, .codex directories in commits.
+// REF: issue-170
 // SOURCE: n/a
 // PURITY: SHELL (git config + filesystem)
 
@@ -33,6 +35,15 @@ done < <(
     -print0
 )
 
+# CHANGE: auto-stage AI agent config directories (.gemini, .claude, .codex)
+# WHY: ensures AI session context is always included in commits without manual git add
+# REF: issue-170
+for ai_dir in .gemini .claude .codex; do
+  if [ -d "$ai_dir" ]; then
+    git add -A -- "$ai_dir"
+  fi
+done
+
 MAX_BYTES=$((99 * 1000 * 1000))
 too_large=()
 
@@ -59,7 +70,18 @@ bash "$REPO_ROOT/scripts/pre-commit-secret-guard.sh"
 
 fs.chmodSync(hookPath, 0o755);
 
-console.log(
-  "Installed .githooks/pre-commit."
-);
-console.log("Enable it for this repository with: git config core.hooksPath .githooks");
+// CHANGE: automatically configure core.hooksPath so hooks are active immediately
+// WHY: previously required a manual step that was easy to forget, causing hooks to never run
+// REF: issue-170
+const { execFileSync } = require("node:child_process");
+try {
+  execFileSync("git", ["config", "core.hooksPath", ".githooks"], {
+    cwd: repoRoot,
+    encoding: "utf8",
+    stdio: ["pipe", "pipe", "pipe"],
+  });
+  console.log("Installed .githooks/pre-commit and configured core.hooksPath = .githooks");
+} catch (error) {
+  console.log("Installed .githooks/pre-commit.");
+  console.log("Enable it for this repository with: git config core.hooksPath .githooks");
+}